Repositories list

• dairy-hpai-monitoring

  Public
  Real-Time Monitoring of HPAI Detections in One or More Dairy Products in the United States

  Python

  •

  GNU General Public License v3.0

  •2•9•0•0•Updated Sep 26, 2025Sep 26, 2025

• mhc_genotyper

  Public
  MHC Class I and II genotyper for Non-Human primates with high-accuracy short reads

  Jupyter Notebook

  •

  Other

  •0•1•0•0•Updated Sep 24, 2025Sep 24, 2025

• geneious-plugin-sra-search

  Public
  NCBI SRA Search plugin for Geneious Prime - Search and download SRA datasets directly in Geneious

  Java

  •

  Other

  •0•1•0•0•Updated Aug 13, 2025Aug 13, 2025

• htcondor_basecalling

  Public
  Shell scripts, submit files, and dag files for basecalling Oxford Nanopore signal files on CHTC's HTCondor cluster

  Shell

  •

  MIT License

  •0•1•1•0•Updated Jul 29, 2025Jul 29, 2025

• 2025-github-website-demo

  Public
  A guide to making GitHub-hosted dashboards with Labkey, Python, Shiny, and Quarto. Mirrored in dholk experiment 31023.

  Just

  •

  MIT License

  •0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

• allele-discovery

  Public
  A Snakemake workflow for discovering novel alleles with PacBio HiFi reads

  Python

  •

  MIT License

  •1•0•1•0•Updated Feb 13, 2025Feb 13, 2025

• Lail-et-al-2024-analysis-pipeline

  Public archive
  Fork of the "oneroof" pipeline for Lail et al. 2024

  Python

  •

  MIT License

  •4•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• SRA_wastewater_lineages

  Public
  Legacy repository for the SRA cryptic lineage finder featured in Suarez et al. 2025

  Python

  •1•0•6•0•Updated Dec 18, 2024Dec 18, 2024

• air_qpcr_helpeR

  Public
  Shiny apps that help work with virus qPCR data from air sample cartridges

  R

  •

  Other

  •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

• Library-Rapid-Antigen-Test-Manuscript

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• nanopore-run-info

  Public
  Information your friendly neighborhood bioinformatician will need to help with your Oxford Nanopore run

  0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• iWES-genotyper

  Public
  Python

  •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

• IPD-ref-generator

  Public
  Workflow for generating useful immunological gene allele databases

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jun 11, 2024Jun 11, 2024

• embl-my-gbk

  Public
  Convert a Genbank file with many extraneous Geneious annotations to EMBL format (even with of strict requirements as IPD)

  Python

  •

  MIT License

  •2•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• IPD-converter

  Public archive
  Nextflow pipeline for converting annotated, genbank-formatted novel allele sequences to Immuno Polymorphism Database format

  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 10, 2024Mar 10, 2024

• air-metagenomics

  Public archive
  Analysis Pipeline for Minor and Ramuta et al. 2023: Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings

  Nextflow

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Jan 11, 2024Jan 11, 2024

• AVRL-pango-updator

  Public
  Nextflow Pipeline for Updating and Extending SARS-CoV-2 Lineage Classifications

  Nextflow

  •

  Other

  •0•0•0•0•Updated Jun 19, 2023Jun 19, 2023

• nf-templates

  Public
  Simple NextFlow Templates for Developing your own Workflows

  Nextflow

  •1•0•0•0•Updated Mar 14, 2023Mar 14, 2023

• MHC-II-allele-discovery

  Public
  Nextflow pipeline for discovering new MHC Class II alleles in Rhesus and Cynomolgus Macaques

  Nextflow

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 27, 2023Feb 27, 2023

• Mecklenburg-et-al-2022

  Public
  Data and scripts used to confirm the discovery of a new cynomolgus macaque Hepatitis A virus

  Python

  •0•0•0•0•Updated Feb 15, 2023Feb 15, 2023

• Frequent-first-trimester-pregnancy-loss-in-rhesus-macaques-infected-with-African-lineage-Zika-virus

  Public
  We found that infection with 1X10^4 PFU ZIKV-DAK at GD30 resulted in pregnancy loss between GD 42 and GD 51 with rates of 100% for SIV+/ZIKV+ dams +ART (n=3), 50% for ZIKV+ +ART (n=3), and 100% for ZIKV+ dams -ART treatment (n=5).

  1•0•0•0•Updated Nov 3, 2022Nov 3, 2022

• E484T-visualizations

  Public
  Data visualization for manuscript on persistent infection that led to globally unique E484T mutation

  R

  •1•0•0•0•Updated Sep 29, 2022Sep 29, 2022

• prolonged-infection-suppfig1

  Public
  Pipeline for examining Intrahost Nucleotide Variants for Halfmann et al. 2022

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 7, 2022Sep 7, 2022

• prolonged-infection-suppfig2

  Public
  Pipeline for visually comparing mutations in a persistent SARS-CoV-2 infection with the virus globally

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 7, 2022Sep 7, 2022

• SARS-CoV-2-Spike-RBD-Analysis

  Public
  Workflow for analyzing SARS-CoV-2 spike RBD amplicon Illumina data.

  Python

  •0•0•0•0•Updated Jul 13, 2022Jul 13, 2022

• MHC_MiSeq_Genotyping_Databases

  Public
  0•0•0•0•Updated Sep 10, 2021Sep 10, 2021

• SNAILS

  Public
  Small Nucleic Acid Instrument for Long Sequences

  Python

  •0•3•2•0•Updated Aug 25, 2021Aug 25, 2021

• Shortreed-et-al-Supplemental-Code

  Public
  Supplemental Information for Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques

  Python

  •1•0•0•0•Updated Nov 15, 2019Nov 15, 2019